Harry Potter and the Instruments of Mortality
by WhereBeginningsEnd
Summary: Harry, an Immortal wizard who wants to help. Clary, a teenage girl who needs help to get her mother back. What will happen when their paths cross at a party. Will their stories change or is it all part of the Plan.
1. Chapter 1

**AN: Hello Guys, this is Alpha and this is my new story, a crossover between the Mortal Instruments series and the Harry Potter series. I would like to tell everybody that this is so very AU. And I would also like to remind everybody that since this is my story, what I say goes, I disregard canon where it suits me and I make up my own.**

 **/**

 **I'm not sure where I am. All I know is that I got abducted from my home by impeccably dressed gentlemen. They put a bag over my head and took me somewhere. I'm now in a very dark room seated in a very uncomfortable chair. They pulled the bag off my head. In front of me was a table with a sort of contract on it. A man walks in. He sits across from me and says "You will sign over the rights to the Harry Potter and Mortal Instrument series."**

 **I gaped at him "I don't own either of those series!"**

 **"Well apparently not. I see you made a post on that did not have a disclaimer. Don't lie to us. Sign it over and we might not torture you!"**

 **"I promise; I don't own either of those series! Please you have to believe me!"**

 **The man sighed, "Take him away and make him confess."**

 **Next thing I know I was being dragged out of the room and pushed into another white padded one. There was a bright light in the top of the room. Then the most horrible sound started to blare throughout the room. "Friday" by Rebecca Black.**

 **\**

 **City of Bones**

 **During Magnus' Party**

"I was proud of my work on you," Magnus said slowly, looking at Clary. "So clean. So perfect. What you saw you would forget, even as you saw it. No image of pixie or goblin or long-legged beastie would remain to trouble your blameless mortal sleep." Magnus was about to say something else but he was interrupted. A man emerged from the shadows, seemingly out of nowhere. He had black hair and emerald green eyes. His face was handsome and he was dressed in a green and silver suit that complemented his eyes.

"Now Magnus, what have I said about bragging." The man spoke in a rich deep British accent.

Jace and Alec tensed at the sight of the man, their hands reaching for their weapons. Clary just looked at him with an unidentifiable look on her face. Magnus just looked at the man and bowed his head. "To do it as often as I could."

The man laughed. "It is good to see that you have not forgotten my lessons." He turned to look at the three teenagers, looking each of them in the eyes. Then he smiled, "How rude of me. Allow me to introduce myself. I am Harry Potter, unlike my young friend, I am not a warlock."

"I am 700 years old!" Magnus said, clearly irritated at being called young.

Harry smiled. "Like I said. So very young." He said this as if he was speaking to a teenager who thought they had it all figured out.

Harry then turned to Clary and smiled. "Clearly Magnus will not introduce you, so I'm afraid you will have to do it yourself."

This snapped Clary out of her thoughts and introduced she herself, "Hello, I'm Clary Fray, these guys are Jace Wayland and Alec Lightwood."

"How wonderful to meet you Clary." Harry smirked and she blushed. "It seems to me as if you have a problem. Would you like to tell me about it, maybe I could be of some service to you?"

"How can you help you help her when you aren't even a Warlock?" Jace said this condescendingly.

Harry looked Jace in the eyes and stared at him for a minute. Then he spoke, "Jace Wayland, Shadowhunter extraordinaire. Someone who thinks they had a hard life because daddy killed his bird."

Jace looked shocked but Harry kept talking, "I can help because I am not a Warlock, I am something much, much older, much more powerful. I was here when the first humans were banished from the garden of Eden. I was there when Johnathan Shadowhunter summoned the Angel Raziel."

At this he paused and smirked. "Who do you think told Johnathan how to summon the Angel."

Jace was about to say something when someone cleared their throat.

It was Magnus. "I would be quick about it if I were you. It is not everyday someone gets a favor from Harry Potter."

Harry just smiled "Yes, I do rarely offer my help in these things, however, something tells me that I will not be able to resist any more requests from the beautiful young woman." He said the last part smiling at Clary. It was a sincere smile.

Clary blushed again but started talking, "Thank you for you offer Mr. Potter- "

"Harry please"

"Harry. Well you see I need to get my memories back so that I can save my mom, but Magnus hid them away and I wanted to know if I could get them back somehow but now I doubt it since apparently it was his masterpiece."

Harry looked at Magnus. "Perfect you said?"

Magnus nodded.

"Well, we will see about that." He looked at Clary again. "I can help but it will be slightly painful. Like a really, really bad headache."

"Please."

Harry smiled. "Now you might want to lie down."

Clary complied. Jace moved forward and whispered to Clary "You don't even know the dude. How do you know you can trust him?"

She looked at him and answered "What other choice do I have?"

Jace and Alec just stood back, staying silent.

"What I am about to say is important so you must listen. When I perform this spell you will see a door. You must open the door to regain your memories. It will try to keep you away but you must fight it. This magic I am about to use is unique. Unique to me and it will be painful. Not physically but mentally. You will fall asleep for a minimum of two hours not anything lesser. Now prepare your mind. Clear it of all thoughts." Harry spoke in a calm hypnotic voice, "Clear your thoughts of all distraction. Breathe, In, Out, In, Out." He flicked his wrist and an ornately beautiful and powerful stick came out. He looked her in the eyes and pointed the stick at her head and said a single word. "Legilimens!"

 **Clary's Mind**

Clary was drawn into her mind. It was as if she was walking through her own memories. Then she saw the door. It was a silver door, carved on it were small pictures, too small to make out. She was about to take the door knob in her hand when suddenly her surroundings changed. The door was still there but so was her mother, Luke and Simon.

"Hey sweetie, where have you been? We've been looking for you!" Her mother said in a concerned voice.

She was about to move forward and hug her mother but a voice in her head said something, "Clary, get to the door. You must open the door. It's not real."

Clary snapped out of it. Luke and Simon looked concernedly at her. She took one last look at all of them and said "I'm sorry. I promise I'll get you back mom. I promise." A tear slid off her cheek. With that, she pulled the door open and stepped through.

 **Back at Magnus' Party**

Harry stepped back. He looked at Magnus and whistled appreciatively, "Very good job Magnus. Very good job. To think, I actually had to exert some effort to break that."

He looked to Jace and Alec "She will be asleep for the next two hours. I would advise against moving her, as she is currently being bombarded by her missing memories. Oh and I would suggest returning to the party Magnus, before it dies down."

Magnus nodded and left.

"I should probably check on Izzy and the mundane." Alec said before he left. Jace just nodded, he was still looking at Clary.

Harry looked at Jace intently before he turned around waving his wand around Clary's body. He spoke softly, "You should check on your friends you know."

"I'm not leaving until she wakes up."

"I will be here when she wakes up and she will still be here when you come back. I promise not to do anything that will hurt her while you are gone, now go and party or whatever. There are still some 2 hours to go before she wakes up, most likely more since her memories were taken rather liberally for the past 12 or so years from what I could tell." Harry spoke in the same soft voice.

Before Jace could respond Alec, Magnus and a girl, who must have been the Izzy Alec was talking about earlier, stepped into the room. They looked angry. Well, Alec and the girl looked angry, Magnus just looked bored.

They stepped into a corner of the room and spoke quietly. Harry could only hear tidbits of the conversation.

"… took Simon…"

"… turned into a rat…"

"… Vampires went to Hotel Dumont…"

"… get him before she wakes up…"

Jace turned around to face Harry and said "We have to go get a stupid mundane that was taken by Vampires."

"A mundane? For what?"

"The mundane was Clary's best friend."

"Well then by all means go. Magnus will show you out." Magnus practically dragged them out.

Harry drew the stick from his sleeve and waved it around her body and it glowed a shimmering gold, like a divine shield protecting her body. "Huh, what would vampires want with a mundane?"

 **I know, a bit of a cliff. I won't let you guys fall off. Don't worry. If there are any grammatical errors, I apologize. I do not have a beta. This will be a full on story, not just one of my vague beginnings. It will become detailed. Throw the rule book out of the window on this one. I hope you guys like it. Constructive Criticism please. And Chapter Two will be up in a week. I project about 15-30 chapter and I am planning to have at least 100k words for this story. I also might do POVs to make it easier. Tell me what you would prefer.**

 **With my love, Alpha**


	2. Chapter 2

**Chapter 2**

 **A/N: So guys… I sincerely apologize. I did not mean for it to be this long for my next update. One week I think I said. Most of the things I had already written were corrupted when I placed my USB drive in the washer soon after I published the first chapter. After that I kind of gave up. The lost work was almost painful for me. But still it was too long. I started writing two weeks ago and haven't stopped since. Forgive me for the wait and as a reward for your patience I give you a chapter and a special disclaimer that for some reason has gained a life all on its own.**

 **Disclaimer:**

 **Pulled out of the room that had been my home for the past year I felt relief. Relief at the release from the torture chamber that, for the past couple of weeks consisted of a replay of whatever i say repeated mockingly back at me with an image of spongebob with a beak and the words that I say in messed up capitalization.**

 **After a few minutes of being dragged down a maze of hallways, my captors push me inside a room and sitting inside was the same man. The same man from a year ago and he looked like he had aged decades but he could still be recognizable as the man I saw a year ago.**

" **Damn you look like you've been through hell in a year!" I say to him.**

 **He just looked at me ever so calm and serious. "2016 was, a hell of a year. And not in a good way. My new boss… well let's say he's a bit inexperienced… in everything. But forget about that. Are you ready to sign over those series now?"**

 **I shake my head, "Things haven't changed since the last time we met Bob. And I hope you don't mind if I call you Bob seeing as you have never given me a name." I sit down at a chair facing "Bob" and continue, "I still don't own those series. Or those characters. Don't you think someone would have noticed I was missing if I was?"**

" **Bob" chuckled, "Oh they might have but a few well placed, shall we say 'fatal illnesses' took people's' attention away. Now sign it over." He seemed to want to try another route this time, "Isn't it a shame that those women take credit for your work? That they gain fame while you rot?"**

 **I groaned exasperatedly at him. "For god's sake man! They are wonderful women who wrote those books on their own and through no way did I participate in its creation. I don't own them and you can take that to the bank!"**

 **He looked sadly at me, "Very well… Maybe a change of entertainment?" His phone rings and as I am being dragged away I hear him say "Yes President Tr…" and the door closed before I could hear anymore.**

 **I found myself in my room again. Everything was black until the pink lights came on and it began… "I'm a Barbie Girl in a Barbie World…" I screamed though I knew very very well that none would hear me.**

 **Still At Magnus' Party/ Harry's POV**

A sigh leaves my lips. I make the decision to enter back into the world, properly, and all this business begins. A day in the life of Harry Potter.

I cast my protective spell and I wonder what is so special about this girl. Looking down at her I could see her innate strength, but also the fragility in her. How close she is to breaking. Well, I certainly couldn't blame her, what with all those revelations in the last couple of days. Still, nothing particularly unique. Maybe that is yet to be seen.

Conjuring a book I began to read. Not 10 minutes passed into my reading when I decided to do something impulsive. Waving my wand around her again to make sure the girl was secure and then I called Magnus.

"Yes, Harry?" Magnus asked with a raised eyebrow.

I pointed at Clary, "Watch her, make sure she is not disturbed. If this place comes under attack, well… you know how to reach me," and with that I turned on the spot and apparated away. And after a moment in the tube I felt my feet touch the ground. As I survey the surrounding area I see that I am right on time as the Shadowhunters arrive with their weapons drawn.

"What are you doing here?" the blond shadowhunter asked, "You're supposed to be protecting Clary!"

"Relax, she is perfectly fine. I have placed her under Magnus' protection." I placated. "I am here to help, I will get you inside then I will leave." As I'm talking to him I am struck by how much he looks like a younger Gellert Grindelwald. Oh had Albus seen this boy he would have nailed him on a wall. And not in a bad way. Ooh bad image! Bad Harry! He seems to notice that I'm staring at him.

"I apologize. It's just, you remind me of somebody." I turn to look at the decrepit old building. Hotel Dumont or should I say Hotel Dumort. No proper entrance. The roof should do. It seems the girl shadowhunter has also noticed that there is not ground entrance. "Jace come on, we need his help if we want to save Simon."

I rub my hands together, "Shadowhunters, if you would like to save that rat boy I would suggest you grasp my arm." They did as I asked and I disapparated onto the roof. And we landed with a quiet whoosh. Well I landed, the rest fell.  
"I apologize for that but it was the quickest way to get you here. Vomit if you must. Call me and I shall arrive to get you. OR call me if you need help. Either one is fine. And do remember that youth means nothing in this building." With that, I turned away from them and jumped off the roof. And I landed on my butt in the chair in front of Clary.

She was still asleep. There was a little bit more than an hour left in her nap. She looked more peaceful now, less confused, as if the memories were coming together. Her memories were tricky things, they would have to stitch themselves back together. The mundane with the fantastical. Well, it would be best to let her sleep, so again I pull out my book and start reading. It was 30 minutes later that i felt a call. Someone was calling my name and it felt urgent.

Getting up, I vanish the book and disapparate. I appear in front of a mass of Vampires surrounding the Shadowhunters who, I assume, are the ones who called my name.

"My… my… what do we have here? A mass of young vampires about to consume three shadowhunters? The Covenant Accords will be quite a mess this time around I see." I say rather loudly so that everyone's attention is on me.

A young latino boy, or someone who appears to be a young latino boy, moves forward. "Who are you?"

"I am no one of real concern. Yet." I slap my hands together and a red wave emanates from them and a moment after, every vampire in the room is on the floor, stunned.

The Shadowhunters look around the room as stunned as the vampires on the floor. The black haired boy was the one who spoke first. "How did you do that? I have never seen a warlock do that before!"

I grin at him. "Wizard magic. If you would like me to say anything further I suggest you wait until we arrive back at Magnus's place. Where's the rat?"

The girl holds up a wiggling brown rat and it looks a bit like scabbers actually. Hmm. Enough of those thoughts.

"You know what to do everyone. Hold onto my arm." Once they had, we were gone with a pop.

We landed back in the room where Clary was resting. Magnus standing beside her bed, a watchful guardian. Or so it appeared. With a wave of my hand the illusion dissipated. Sighing i call for Magnus. That child. When he finally appeared I smacked him on his head. "I leave you to protect her and you leave an illusion in your place?"

He looks at me with not a sign of regret for his actions. "Like anyone could have broken through that shield of yours. It's not of this world."

I sighed. Honestly he wasn't wrong. With a shake of my head I clear it. I looked down at her. It looked as if she was ready to come out. Only a few memories left. The most recent. I draw my wand and remove the shield.

Turning to the Shadowhunters I spoke. "She will be awake soon. Now before I answer any questions you may have, would you like to introduce yourselves so that I do not have to call you blond shadowhunter or black haired male shadowhunter or black haired female shadowhunter?"

The girl went first. "I am Isabelle Lightwood."

Then the black haired boy. "I'm Alec Lightwood."

And finally the blond one. "I'm Jace… Jace Wayland."

I looked at him intently, scanning his features for the second time that night. "You do not look like a Wayland."

"Yeah? Well you don't look like a wizard." Jace snapped back.

I smile, "And how would you think a wizard dresses? In robes and a pointy hat?" A snap of my fingers later and I am not clad in robes and my old pointy hat. I grew a long white beard with it. "Yes I could dress this way but why would I?" And with a gesture I was back in my normal clothes.

"I am a wizard. Fully human, no demon blood in me whatsoever. Some venom from a poisonous snake and tears from an immortal firebird, but no demon blood… or angel blood for that matter. I just don't happen to be from this dimension, or universe, whatever you want to call it."

Jace looked intrigued, "When did you arrive here? How old are you?"

"I arrived when the first humans were created. Adam and Eve. I witnessed there banishment, their procreation. I was there when everybody suddenly didn't speak the same language. I was there for the flood. There when the wars started. There when the crusaders needed heavenly help after demons crossed into this world. I created the ritual to summon raziel. At the beginning of the 19th century however, I began to draw back from the world. To see if some of the recent historical events I know did happen on my world would." I close my eyes as the memories of my nearly forgotten world surfaced. I open my eyes and put a smile on my face. "I tinkered a bit. Saved those who I thought worthy. Today I made the choice to come back and what a day it has been. ANyway that's enough about my story. Your friend should be waking up just about now."

And true to my word Clary's eyes opened and with a gasp she awoke. Her first words however were quite surprising to them, "I know where the Mortal Cup is."


	3. Chapter 3

**AN: Guys! I am stunned at the response this fic has gotten while I have been gone. I apologize extremely for the length of time I've taken on moving forward with this fic. I have no excuses other than a lack of motivation and inspiration. Let's see how far I get before I run out of motivation shall we?**

 **Disclaimer: I was awoken with a cold bucket of water that had been a substitute for a shower for what I would later remember to be the last day of my wretched stay in that dratted building. Anyways, as soon as I cleared my head of the last remnants of sleep I looked at Barry, the man who usually gave me my wakeup call.**

" **Hey Bar, good to see you back. How was the holiday?" I asked.**

 **He smiled at me, "Pretty well actually. Good to spend some time with my family finally, it feels like it's been years since we've gone on a proper vacation together."**

 **I rubbed my hands together and nodded at him, "Well that's good. Now its getting time for you to leave isn't it? Time for my torture to resume."**

 **He grimaced, "Yes… well I hear that they've updated the torture should be an interesting first few times, right?" He moved towards the door and opened it. "Well I'll leave you to it."**

 **It was at that moment when something miraculous yet slightly disturbing happened. Barry stopped suddenly, looked at me and said, "Hey Alf I don't feel so good."**

 **I looked at him perplexedly when he started disintegrating into tiny black specks. I saw the pile on the floor. I took that as a sign from the gods and ran from the room quickly giving a silent prayer for Barry who throughout his imprisonment had kind of become his anchor.**

 **AN: Well it seems my disclaimer travels have certainly kept up hasn't it? Well I've decided to not do the first-person thing again because I don't think it went well and as I've been gone I've been improving my writing style and I don't think that first person is for me. Anyways enough of me blathering on… Enjoy**

Everyone in the room seemed some form of relieved when Clary awoke. Well, everyone except Alec. Then what she said registered into the minds of the Shadowhunters. Before they could move Harry moved forward and cast several spells on her. He smiled soon after he finished casting.

"Well it seems that you've recovered fully from your ordeal I think you're prepared to finish this little quest of yours." Harry smiled at her.

Clary looked at Jace and he gave her a nod. Clary got up with a helping hand from Harry and what neither saw was Jace glaring at the contact. He might not have liked that, but it got worse when Clary gave Harry a hug. "Thank you, Mr. Potter, for your help."

Jace coughed, "I think its time that we get a move on Clary before Valentine's men find out and get there before us."

Harry pulled away from the hug and laughed, "Yes well I do believe you are most welcome Clary. Now before you go running off perhaps you'd like to explain to your friends where you're going first? If time really is a factor, then perhaps I can help you get there faster?"

"You can do that?" Clary shook her head, "Never mind, stupid question. I, we, have to go home. They are with my neighbor, she has them."

Harry nodded, "Well I've seen your home from your mind and I think I can make a portkey to it, a sort of object that can pull you to your destination. Sort of like your portals? But… not nearly as pleasant but definitely quicker."

He conjured a rope and then cast Portus at it. "Everyone who wishes to go touch the rope." Everyone did so, and Harry let it go and said "Good now I'll leave you to it. Good luck everyone. Au revoir." With those words the portkey activated and dragged them away from his sight.

Harry looked at Magnus, "It has been an eventful night hasn't it."

Magnus glared at his old master, "Yes, well any night you choose to come out of your self-imposed exile is bound to be exciting. Why now? And don't bother giving that excuse you gave the children. You knew a thousand years ago that it wouldn't go as you hoped. So… why now?"

"I felt it Magnus, Death. They wanted me to be here tonight. I think old man upstairs has called in a favor or two as well and it felt right helping her."

With a shake of his head, Magnus left the room while looking over his shoulder, "I guess I should prepare my warlocks. They should be ready if you've come out of the woodwork."

Harry laughed at the cheeky, if accurate comment. He sat down and closed his eyes. It would be a while before he got accustomed to being out and about again. He couldn't wait for the reactions from the Underworlders and Shadowhunters alike when they heard of his return, if they even knew he existed at all.

'Who knew teenagers could be so incompetent that they couldn't even deal with a demon.' Was Harry's thought process as he summoned his wand and summoned his armor to himself, leather from a great demon's carcass in the form of a cassock. He then twisted in place and arrived in front of the demon Abaddon in the Sanctuary shielding Clary.

Harry grinned savagely, "My dear Abaddon! Its been centuries."

That stopped Abaddon in his tracks. "Potter? What are you doing here!? You've stopped interfering. It does not matter. You too will fall." With that Abaddon advanced on Harry causing Jace to miss the stab he had been aiming while Abaddon seemed distracted by the arrival of Harry. The Shadowhunters were stunned at the magic showcased.

With a flourish of his wand and a jab a Reducto was flying towards the demon. The demon, with surprising speed belying his size dodged the spell and the many others that followed it.

"Do you recognize my outfit Abaddon?" Harry taunted the Great Demon whose skin made up his cassock. Abaddon growled and rushed at Harry who hadn't moved since he arrived, still protecting Clary with his body. With an open palm push to the front harry summoned a great shield that stopped Abaddon in his tracks.

Harry tutted at the demon. "Have you forgotten how susceptible you are to my magic?" With an aggressive twirl as if encircling of his wand the demon was tied together by bands of light.

The demon screamed as his skin was burned by the bands of pure magic. Harry pulled an ornate glaive with runes running along the pole and blade and made to cut off Abaddon's head, but the demon broke the bands with his talons.

"I have strengthened since our last meeting Potter." Abaddon growled as he tensed his muscles readying for an attack. He struck at Harry, but Harry blocked with his glaive and spun out of his reach.

With a smile harry replied, "Well a little more effort will be needed then. He moved forward and swung the blade at Abaddon who parried with his own talons, surprisingly strong enough to resist the enchanted steel."

A raised eyebrow from Harry showed his surprise at their withstanding his swing. That had not happened last time, Harry distinctly remembered. He decided on another course of action to end this quickly before the boy who was bleeding perished. He struck with a clenched fist empowered with a bludgeoner curse forcing the demon back.

He summoned his wand and with a whisper cast his favorite charm, "Expecto Patronum." And his brilliant light stag moved forward and without any prompt from harry, Prongs advanced and gored Abaddon with the horns he had been named for. The others around the room felt lightened at the aura and with a unanimous gasp as Abaddon disintegrated before their eyes.

With a congenial smile that made it hard to equate his strength and ease that destroyed a great demon, Harry looked at all of them. His smile did not last when he saw the black-haired girl cradling the black-haired boy's head. Alec and Isabelle if he remembered correctly. He moved towards them and kneeled over him and waved his wand around his body using diagnostic spells.

"The poison from the scratch is spreading. I can stop it, but I must have permission." Harry looked at Isabelle.

Isabelle could only nod.

"Very well." Harry held his wand in hand and performed several arm movements that left a string of fire. Soon the fire started to form the image of a lightning bolt. He used his wand to cut his palm open and held Alec's jaw open. He dribbled in some of his blood into Alec's mouth.

Alec gave a deep groan of pain and struggled against his sister's hold but soon relaxed, his pain fading as the poison in his blood was removed.

Shaking his head Harry regarded them, children, barely out of their diapers and yet here they were fighting demons and trying to save the world. But then again, they were older than he was when he first fought, killed even. Shaking his head again, this time to clear his thoughts he stood up.

"Return to the institute. The boy is not yet free from the poison and I have a feeling much will be revealed there. I cannot aid you inside the institute as I require permission to enter private abodes." Harry told them. "Go now. I will send Magnus to help the boy more. The poison is still within him. It seems my blood was not as effective for him as it had been for others."

Clary moved towards Alec with guilt in her eyes, "Couldn't you transport us? So we can get there quicker?"

Harry shook his head, "I'm not a delivery service Clary. I cannot take you to the Institute with my magic. The protections at the Institute have not been tested by my magic and I would not know the effect they have on a portkey or apparition. Drive there and you will be safe."

Harry made to leave but a call stopped him.

"Harry… thank you." Clary said in a shy voice, "Thank you for saving us, for helping us."

With a smile he simply said, "It was my pleasure." And he was gone.


End file.
